PathVisio 3: an extendable pathway analysis toolbox
Kutmon, Martina, van Iersel, Martijn P, Bohler, Anwesha, Kelder, Thomas, Nunes, Nuno, Pico, Alexander R, Evelo, Chris T
Published in PLoS computational biology (01.02.2015)
Published in PLoS computational biology (01.02.2015)
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Journal Article
Presenting and exploring biological pathways with PathVisio
van Iersel, Martijn P, Kelder, Thomas, Pico, Alexander R, Hanspers, Kristina, Coort, Susan, Conklin, Bruce R, Evelo, Chris
Published in BMC bioinformatics (25.09.2008)
Published in BMC bioinformatics (25.09.2008)
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Journal Article
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
van Iersel, Martijn P, Pico, Alexander R, Kelder, Thomas, Gao, Jianjiong, Ho, Isaac, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris T
Published in BMC bioinformatics (04.01.2010)
Published in BMC bioinformatics (04.01.2010)
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Journal Article
Mining biological pathways using WikiPathways web services
Kelder, Thomas, Pico, Alexander R, Hanspers, Kristina, van Iersel, Martijn P, Evelo, Chris, Conklin, Bruce R
Published in PloS one (30.07.2009)
Published in PloS one (30.07.2009)
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Journal Article
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
Terfve, Camille, Cokelaer, Thomas, Henriques, David, MacNamara, Aidan, Goncalves, Emanuel, Morris, Melody K, van Iersel, Martijn, Lauffenburger, Douglas A, Saez-Rodriguez, Julio
Published in BMC systems biology (18.10.2012)
Published in BMC systems biology (18.10.2012)
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Journal Article
WikiPathways: pathway editing for the people
Pico, Alexander R, Kelder, Thomas, van Iersel, Martijn P, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris
Published in PLoS biology (01.07.2008)
Published in PLoS biology (01.07.2008)
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Journal Article
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Chaouiya, Claudine, Bérenguier, Duncan, Keating, Sarah M, Naldi, Aurélien, van Iersel, Martijn P, Rodriguez, Nicolas, Dräger, Andreas, Büchel, Finja, Cokelaer, Thomas, Kowal, Bryan, Wicks, Benjamin, Gonçalves, Emanuel, Dorier, Julien, Page, Michel, Monteiro, Pedro T, von Kamp, Axel, Xenarios, Ioannis, de Jong, Hidde, Hucka, Michael, Klamt, Steffen, Thieffry, Denis, Le Novère, Nicolas, Saez-Rodriguez, Julio, Helikar, Tomáš
Published in BMC systems biology (10.12.2013)
Published in BMC systems biology (10.12.2013)
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Journal Article
Increasing Soy Isoflavonoid Content and Diversity by Simultaneous Malting and Challenging by a Fungus to Modulate Estrogenicity
Simons, Rudy, Vincken, Jean-Paul, Roidos, Nikolaos, Bovee, Toine F. H, van Iersel, Martijn, Verbruggen, Marian A, Gruppen, Harry
Published in Journal of agricultural and food chemistry (22.06.2011)
Published in Journal of agricultural and food chemistry (22.06.2011)
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Journal Article
Software support for SBGN maps: SBGN-ML and LibSBGN
van Iersel, Martijn P, Villéger, Alice C, Czauderna, Tobias, Boyd, Sarah E, Bergmann, Frank T, Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I, Mi, Huaiyu, Moodie, Stuart L, Kitano, Hiroaki, Le Novère, Nicolas, Schreiber, Falk
Published in Bioinformatics (01.08.2012)
Published in Bioinformatics (01.08.2012)
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Journal Article
WikiPathways: building research communities on biological pathways
Kelder, Thomas, van Iersel, Martijn P., Hanspers, Kristina, Kutmon, Martina, Conklin, Bruce R., Evelo, Chris T., Pico, Alexander R.
Published in Nucleic acids research (01.01.2012)
Published in Nucleic acids research (01.01.2012)
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Journal Article
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations
CHANDAN, Kumar, LERSEL, Martijn P. Van, ALADJEM, Mirit I, KOHN, Kurt W, LUNA, Augustin
Published in Bioinformatics (Oxford, England) (15.03.2012)
Published in Bioinformatics (Oxford, England) (15.03.2012)
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Journal Article
Integrated visualization of a multi-omics study of starvation in mouse intestine
Iersel, Martijn P. van, Sokolović, Milka, Lenaerts, Kaatje, Kutmon, Martina, Bouwman, Freek G., Lamers, Wouter H., Mariman, Edwin C.M., Evelo, Chris T.
Published in Journal of integrative bioinformatics (01.03.2014)
Published in Journal of integrative bioinformatics (01.03.2014)
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Journal Article
BridgeDb app: unifying identifier mapping services for Cytoscape
Gao, Jianjiong, Zhang, Chao, van Iersel, Martijn, Zhang, Li, Xu, Dong, Schultz, Nikolaus, R Pico, Alexander
Published in F1000 research (2014)
Published in F1000 research (2014)
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Journal Article
Path2Models: large-scale generation of computational models from biochemical pathway maps
Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B, Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, Le Novère, Nicolas
Published in BMC systems biology (01.11.2013)
Published in BMC systems biology (01.11.2013)
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Journal Article
The systems biology format converter
Rodriguez, Nicolas, Pettit, Jean-Baptiste, Dalle Pezze, Piero, Li, Lu, Henry, Arnaud, van Iersel, Martijn P, Jalowicki, Gael, Kutmon, Martina, Natarajan, Kedar N, Tolnay, David, Stefan, Melanie I, Evelo, Chris T, Le Novère, Nicolas
Published in BMC bioinformatics (05.04.2016)
Published in BMC bioinformatics (05.04.2016)
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Journal Article
The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation
Baccini, Michela, Bachmaier, Eva-Maria, Biggeri, Annibale, Boekschoten, Mark V, Bouwman, Freek G, Brennan, Lorraine, Caesar, Robert, Cinti, Saverio, Coort, Susan L, Crosley, Katie, Daniel, Hannelore, Drevon, Christian A, Duthie, Susan, Eijssen, Lars, Elliott, Ruan M, van Erk, Marjan, Evelo, Chris, Gibney, Mike, Heim, Carolin, Horgan, Graham W, Johnson, Ian T, Kelder, Thomas, Kleemann, Robert, Kooistra, Teake, van Iersel, Martijn P, Mariman, Edwin C, Mayer, Claus, McLoughlin, Gerard, Müller, Michael, Mulholland, Francis, van Ommen, Ben, Polley, Abigael C, Pujos-Guillot, Estelle, Rubio-Aliaga, Isabel, Roche, Helen M, de Roos, Baukje, Sailer, Manuela, Tonini, Giulia, Williams, Lynda M, de Wit, Nicole
Published in Genes & nutrition (01.12.2008)
Published in Genes & nutrition (01.12.2008)
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Journal Article
CySBGN: a Cytoscape plug-in to integrate SBGN maps
Gonçalves, Emanuel, van Iersel, Martijn, Saez-Rodriguez, Julio
Published in BMC bioinformatics (16.01.2013)
Published in BMC bioinformatics (16.01.2013)
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Journal Article
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Bohler, Anwesha, Eijssen, Lars M T, van Iersel, Martijn P, Leemans, Christ, Willighagen, Egon L, Kutmon, Martina, Jaillard, Magali, Evelo, Chris T
Published in BMC bioinformatics (23.08.2015)
Published in BMC bioinformatics (23.08.2015)
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Journal Article
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways
Fried, Jake Y, van Iersel, Martijn P, Aladjem, Mirit I, Kohn, Kurt W, Luna, Augustin
Published in Bioinformatics (01.06.2013)
Published in Bioinformatics (01.06.2013)
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Journal Article
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)
Luna, Augustin, Sunshine, Margot L., van Iersel, Martijn P., Aladjem, Mirit I., Kohn, Kurt W.
Published in Bioinformatics (01.08.2011)
Published in Bioinformatics (01.08.2011)
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Journal Article